Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge

Environmental Microbiology

Volumn 5, Issue 10, 2003, Pages 961-976

  López García, Purificación ^a   Duperron, Sébastien ^b,e   Philippot, Pascal ^c   Foriel, Julien ^c   Susini, Jean ^d   Moreira, David ^a  

^a UNIVERSITÉ PARIS SUD   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c INSTITUT DE PHYSIQUE DU GLOBE DE PARIS   (France)

^d EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

^e TECHNOPÔLE BREST IROISE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

IRON; PUMICE; RNA 16S; SEA WATER; SILICATE;

ARTICLE; ATLANTIC OCEAN; CLASSIFICATION; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; GENETIC VARIABILITY; GENETICS; HEAT; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEDIMENT; SPECTROSCOPY; STATISTICAL MODEL;

ATLANTIC OCEAN; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; GEOLOGIC SEDIMENTS; HEAT; IRON; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SILICATES; SPECTRUM ANALYSIS; VARIATION (GENETICS); WATER MICROBIOLOGY;

ACIDOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDES; CYTOPHAGA; DELTAPROTEOBACTERIA; ENVIRONMENTAL SEQUENCE; EPSILONPROTEOBACTERIA; FLAVOBACTERIUM; GAMMAPROTEOBACTERIA; NEGIBACTERIA; NITROSPIRAE; PLANCTOMYCETALES; POSIBACTERIA; PROTEOBACTERIA;

EID: 0141788252     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00495.x     Document Type: Article

References (61)

1. Alain, K., Olagnon, M., Desbruyères, D., Pagé, A., Barbier, G., Juniper, S.K., et al. (2002a) Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiol Ecol 42: 463-476.
2. Alain, K., Querellou, J., Lesongeur, F., Pignet, P., Crassous, P., Raguenes, G., et al. (2002b) Caminibacter hydrogeniphilus gen nov., sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium isolated from an East Pacific Rise hydrothermal vent. Int J Syst Evol Microbiol 52: 1317-1323.
3. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
4. Bowman, J.P., and McCuaig, R.D. (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental self sediment. Appl Environ Microbiol 69: 2463-2483.
5. Campbell, B.J., Jeanthon, C., Kostka, J.E., Luther, G.W., and Cary, S.C. (2001) Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl Environ Microbiol 67: 4566-4572.
6. Cave, R.R., German, C.R., Thomson, J., and Nesbitt, R.W. (2002) Fluxes to sediments underlying the Rainbow hydrothermal plume at 36°14′N on the Mid-Atlantic Ridge. Geochim Cosmochim Acta 66: 1905-1923.
7. Cole, J.R., Chai, B., Marsh, T.L, Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
8. Corre, E., Reysenbach, A.L., and Prieur, D. (2001) Epsilon-proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol Lett 205: 329-335.
9. David, C., Kaulich, B., Barrett, R., Salomé, M., and Susini, J. (2000) High-resolution lenses for sub-100 nm x-ray fluorescence microscopy. Appl Phys Lett 77: 3851-3853.
10. Distel, D.L., Lane, D.J., Olsen, G.J., Giovannoni, S.J., Pace, B., Pace, N.R., et al. (1988) Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J Bacteriol 170: 2506-2510.
11. Douville, E., Charlou, J.L., Oelkers, E.H., Bienvenu, P., Jove Colon, C.F., Donval, J.P., et al. (2002) The rainbow vent fluids (36°14′N, MAR): the influence of ultramafic rocks and phase separation on trace metal content in Mid-Atlantic Ridge hydrothermal fluids. Chem Geol 184: 37-48.
12. Edgcomb, V.P., Kysela, D.T., Teske, A., De Vera Gomez, A., and Sogin, M.L. (2002) Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc Natl Acad Sci USA 99: 7658-7662.
13. Foriel, J., Philippot, P., Cauzid, J., Susini, J., Dumas, P., Khodja, H., et al. (2003) High resolution synchrotron-based imaging of sulfur oxidation states in individual microfossils and contemporary microbial filaments. Geochim Cosmochim Acta (in press).
14. Fuhrman, J.A., and Davis, A.A. (1997) Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Series 150: 275-285.
15. Haddad, A., Camacho, F., Durand, P., and Cary, S.C. (1995) Phylogenetic characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana. Appl Environ Microbiol 61: 1679-1687.
16. Hayashi, N.R., Ishida, T., Yokota, A., Kodama, T., and Igarashi, Y. (1999) Hydrogenophilus thermoluteolus gen nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol 49: 783-786.
17. Hugenholtz, P., Tyson, G.W., Webb, R.I., Wagner, A.M., and Blackall, L.L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl Environ Microbiol 67: 411-419.
18. Jannasch, H.W., and Mottl, M.J. (1985) Geomicrobiology of deep-sea hydrothermal vents. Science 229: 717-725.
19. Jannasch, H.W., Wirsen, C.O., Nelson, D.C., and Robertson, L.A. (1985) Thiomicrospira crunogena sp. nov., a colorless sulfur-oxidizing bacterium from a deep-sea hydrothermal vent. Int J Syst Bacteriol 35: 422-424.
20. Jannasch, H.W., Nelson, D.C., and Wirsen, C.O. (1989) Massive natural occurrence of unusually large bacteria (Beggiatoa sp.) at a hydrothermal deep-sea vent site. Nature 342: 834-836.
21. Jeanthon, C. (2000) Molecular ecology of hydrothermal vent microbial communities. Antonie Van Leeuwenhoek 77: 117-133.
22. Jobb, G. (2002) treefinder. [WWW document]. URL http://www.treefinder.de
23. Kuenen, J.G., Robertson, L.A., and Tuovinen, O.H. (1992) The genera Thiobacillus, Thiomicrospira and Thiosphaera. In The Genera Thiobacillus, Thiomicrospira, and Thiosphaera. Balows, A., Trüper, H.G., Dworkin, M., Harder W., and Schleifer, K.H. (eds). Vol. III, New York: Springer-Verlag.
24. Li, L., Guezennec, J., Nichols, P., Henry, P., Yanagibayashi, M., and Kato, C. (1999) Microbial diversity in Nankai Trough sediments at a depths of 3,843 m. J Oceanogr 55: 635-642.
25. Longnecker, K., and Reysenbach, A. (2001) Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise. FEMS Microbiol Ecol 35: 287-293.
26. López-García, P., López-López, A., Moreira, D., and Rodríguez-Valera, F. (2001) Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol Ecol 36: 193-202.
27. López-García, P., Gaill, F., and Moreira, D. (2002) Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ Microbiol 4: 204-215.
28. López-García, P., Philippe, H., Gaill, F., and Moreira, D. (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental micro-colonizers at the Mid-Atlantic Ridge. Proc Natl Acad Sci USA 100: 697-702.
29. Ludwig, W., Bauer, S.H., Bauer, M., Held, I., Kirchhof, G., Schulze, R., et al. (1997) Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol Lett 153: 181-190.
30. Madigan, M.T., Martinko, J.M., and Parker, J. (1997) Brock Biology of Microorganisms. New Jersey: Prentice Hall.
31. Martin, M.O. (2002) Predatory prokaryotes: an emerging research opportunity. J Mol Microbiol Biotechnol 4: 467-477.
32. McCollom, T.M., and Shock, E.L. (1997) Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta 61: 4375-4391.
33. Miroshnichenko, M.L., Kostrikina, N.A., L'Haridon, S., Jeanthon, C., Hippe, H., Stackebrandt, E., and Bonch-Osmolovskaya, E.A. (2002) Nautilia lithotrophica gen nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 52: 1299-1304.
34. Morris, R.M., Rappe, M.S., Connon, S.A., Vergin, K.L, Siebold, W.A., Carlson, C.A., and Giovannoni, S.J. (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
35. Moyer, C.L., Dobbs, F.C., and Karl, D.M. (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent site, Loihi Seamount, Hawaii. Appl Environ Microbiol 61: 1555-1562.
36. Muyzer, G., Teske, A., Wirsen, C.O., and Jannasch, H.W. (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
37. Nisbet, E.G., and Sleep, N.H. (2001) The habitat and nature of early life. Nature 409: 1083-1091.
38. Norris, T.B., Wraith, J.M, Castenholz, R.W., and McDermott, T.R. (2002) Soil microbial community structure across a thermal gradient following a geothermal heating event. Appl Environ Microbiol 68: 6300-6309.
39. Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.R., and Stahl, D.A. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40: 337-365.
40. Philippe, H. (1993) MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21: 5264-5272.
41. Philippot, P., Foriel, J., Cauzid, J., Susini, J., Ménez, B., and Somogyi, A. (2002) Imaging sulfur-metabolism activities in individual filamentous microfossils. Highlights ESRF 2002: 85-87.
42. Philippot, P., Foriel, J., Susini, J., Khodja, H., Grassineau, N., and Fouquet, Y. (2003) High-resolution imaging of transition metal and sulfur-redox distribution in individual microfossils. J Phys IV 104: 381-384.
43. Polz, M.F., and Cavanaugh, C.M. (1995) Dominance of one bacterial phylotype at a Mid-Atlantic Ridge hydrothermal vent site. Proc Natl Acad Sci USA 92: 7232-7236.
44. Prieur, D. (1997) Microbiology of deep-sea hydrothermal vents. Trends Biotechnol 15: 242-244.
45. Ravenschlag, K., Sahm, K., Pernthaler, J., and Amann, R. (1999) High bacterial diversity in permanently cold marine sediments. Appl Environ Microbiol 65: 3982-3989.
46. Reichenbach, H. (1999) The ecology of the myxobacteria. Environ Microbiol 1: 15-21.
47. Reysenbach, A.L., and Cady, S.L. (2001) Microbiology of ancient and modern hydrothermal systems. Trends Microbiol 9: 79-86.
48. Reysenbach, A.L., and Shock, E. (2002) Merging genomes with geochemistry in hydrothermal ecosystems. Science 296: 1077-1082.
49. Reysenbach, A.L., Longnecker, K., and Kirshtein, J. (2000) Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl Environ Microbiol 66: 3798-3806.
50. Sanford, R.A., Cole, J.R., and Tiedje, J.M. (2002) Characterization and description of Anaeromyxobacter dehalogenans gen nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68: 893-900.
51. Sievert, S.M., Kuever, J., and Muyzer, G. (2000) Identification of 16S ribosomal DNA-defined bacterial populations at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl Environ Microbiol 66: 3102-3109.
52. Snyder, A.R., Williams, H.N., Baer, M.L., Walker, K.E., and Stine, O.C. (2002) 16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity. Int J Syst Evol Microbiol 52: 2089-2094.
53. Stetter, K.O. (1999) Extremophiles and their adaptation to hot environments. FEBS Lett 452: 22-25.
54. Stohr, R., Waberski, A., Liesack, W., Volker, H., Wehmeyer, U., and Thomm, M. (2001) Hydrogenophilus hirschii sp. nov., a novel thermophilic hydrogen-oxidizing betaproteobacterium isolated from Yellowstone National Park. Int J Syst Evol Microbiol 51: 481-488.
55. Susini, J., Salome, M, Fayard, B., Ortega, R., and Kaulich, B. (2002) The scanning X-Ray microprobe at the ESRF 'X-Ray microscopy' beamline. Surface Rev Lett 9: 203-211.
56. Takai, K., Inagaki, F., Nakagawa, S., Hirayama, H., Nunoura, T., Sako, Y., et al. (2003) Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Ecol 218: 167-174.
57. Taylor, C.D., Wirsen, C.O., and Gaill, F. (1999) Rapid microbial production of filamentous sulfur mats at hydrothermal vents. Appl Environ Microbiol 65: 2253-2255.
58. Teske, A., Brinkhoff, T., Muyzer, G., Moser, D.P., Rethmeier, J., and Jannasch, H.W. (2000) Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microbiol 66: 3125-3133.
59. Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., et al. (2002) Microbial diversity of hydrothermal sediments in the Guaymas basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
60. Thar, R., and Fenchel, T. (2001) True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus. Appl Environ Microbiol 67: 3299-3303.
61. Wirsen, C.O., Sievert, S.M., Cavanaugh, C.M., Molyneaux, S.J., Ahmad, A., Taylor, L.T., et al. (2002) Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur. Appl Environ Microbiol 68: 316-325.